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Detailed information for vg0721287216:

Variant ID: vg0721287216 (JBrowse)Variation Type: SNP
Chromosome: chr07Position: 21287216
Reference Allele: TAlternative Allele: C
Primary Allele: TSecondary Allele: C

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 1.00, others allele: 0.00, population size: 281. )

Flanking Sequence (100 bp) in Reference Genome:


ACCCCACTTGCTGCTGTTTTTCTGCAGTTGGTTTATGTGTGTGGAAAATGGTTAGTCAAGCTAGCACTGCCTAACGATATATTAAACCATTTCCTTCCGT[T/C]
TCTTTTGGTGCATGCCTGCATGGTGTTAGGAAACCGAACATCTTCGGTCTGATCATCATCAGCCAGCACGGTGAGACCCAAAGGGACTTTTCTAAAAATA

Reverse complement sequence

TATTTTTAGAAAAGTCCCTTTGGGTCTCACCGTGCTGGCTGATGATGATCAGACCGAAGATGTTCGGTTTCCTAACACCATGCAGGCATGCACCAAAAGA[A/G]
ACGGAAGGAAATGGTTTAATATATCGTTAGGCAGTGCTAGCTTGACTAACCATTTTCCACACACATAAACCAACTGCAGAAAAACAGCAGCAAGTGGGGT

Allele Frequencies:

Populations Population SizeFrequency of T(primary allele) Frequency of C(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 83.00% 16.90% 0.11% 0.00% NA
All Indica  2759 73.40% 26.50% 0.18% 0.00% NA
All Japonica  1512 99.60% 0.40% 0.00% 0.00% NA
Aus  269 93.70% 6.30% 0.00% 0.00% NA
Indica I  595 98.30% 1.70% 0.00% 0.00% NA
Indica II  465 36.80% 62.60% 0.65% 0.00% NA
Indica III  913 77.40% 22.50% 0.11% 0.00% NA
Indica Intermediate  786 71.40% 28.50% 0.13% 0.00% NA
Temperate Japonica  767 99.90% 0.10% 0.00% 0.00% NA
Tropical Japonica  504 100.00% 0.00% 0.00% 0.00% NA
Japonica Intermediate  241 97.90% 2.10% 0.00% 0.00% NA
VI/Aromatic  96 67.70% 32.30% 0.00% 0.00% NA
Intermediate  90 82.20% 17.80% 0.00% 0.00% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0721287216 T -> C LOC_Os07g35560.1 upstream_gene_variant ; 4590.0bp to feature; MODIFIER silent_mutation Average:69.982; most accessible tissue: Callus, score: 94.164 N N N N
vg0721287216 T -> C LOC_Os07g35560.3 upstream_gene_variant ; 4590.0bp to feature; MODIFIER silent_mutation Average:69.982; most accessible tissue: Callus, score: 94.164 N N N N
vg0721287216 T -> C LOC_Os07g35560.2 upstream_gene_variant ; 4579.0bp to feature; MODIFIER silent_mutation Average:69.982; most accessible tissue: Callus, score: 94.164 N N N N
vg0721287216 T -> C LOC_Os07g35560-LOC_Os07g35570 intergenic_region ; MODIFIER silent_mutation Average:69.982; most accessible tissue: Callus, score: 94.164 N N N N

Effects Predicted by Deep Convolutional Neural Networks

For each variant, we constructed two sequences that contain the variation site and the sequence around it, differing only in the variation site. We then used Basenji to predict the chromatin accessibility of each tissue for the two sequences, respectively, and scored the effect of the variant by comparing the changes in chromatin accessibility corresponding to the two genotypes in the 1 kb region around the variation site. The effect score was defined as the logarithmic ratio of the predicted chromatin accessibility of the alternative genotype to the value of the reference genotype.

Var ID Ref Alt Root (RT) Young Leaf (YL) Flag Leaf (FL) Young Panicle (YP) Lemma & Palea (LP) Stamen & Pistil (SP)
vg0721287216 T C 0.13 0.09 0.05 0.05 0.1 0.07

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0721287216 NA 5.10E-14 Grain_length All Not Breeding signatures of rice improvement revealed by a genomic variation map from a large germplasm collection, Proc Natl Acad Sci USA, 112(39): E5411-E5419, PMID:26358652
vg0721287216 8.67E-06 NA mr1477 All YES Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0721287216 8.10E-06 NA mr1477 Ind_All Not Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0721287216 NA 3.63E-09 mr1598_2 Ind_All Not Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251